San Diego County home prices continued their months-long climb in September but at a slower pace than during the summer, the closely watched Standard & Poor’s Case-Shiller Home Price Index showed yesterday.

Mirroring trends elsewhere, San Diego’s index was up 0.9 percent from August, the slowest month-to-month rise since May. But on a year-over-year basis, the 5.7 percent decline was the smallest in more than two years.

Analysts have attributed part of the improved housing market to the federal government’s $8,000 first-time homebuyer tax credit, which was scheduled to end this month. It has been extended to spring and expanded to include some move-up homebuyers.

Michael Lea, director of the Corky McMillin Center for Real Estate at San Diego State University, said the prospects of more defaults and foreclosures might reverse the price rises if owners who are behind in payments are unable to get their mortgages modified.

“That’s a downside risk, but it’s encouraging to see things flattening out and rising in most of the country,” Lea said.

San Diego, while suffering from a 10.5 percent unemployment rate that exceeds the 10.2 percent national rate, is better off than many other metro areas, Lea said.

“San Diego was one of the first markets to go down and it has stabilized more than the really badly affected Sunbelt markets,” he said.

Other analysts expressed concern that millions of homes are still worth less than their mortgage balances, even if prices are off their lows, and that sales of distressed properties will dominate the market this winter as they did last year.

The index, starting at 100 in January 2000, measures price changes on the paired sales of single-family homes. For San Diego the latest index stood at 154.76, compared with 153.34 in August and 164.12 in September 2008. The index reached a peak locally of 250.34 in November 2005 and a low of 144.43 in April.

In other words, San Diego’s resale houses rose to 2.5 times their January 2000 values before falling and are now down 38.2 percent from the peak and 7.2 percent up from the trough. The index stands approximately where it was at the end of 2002.

San Diego-based MDA DataQuick’s monthly price reports are following similar trends. The overall median for September was $325,000, unchanged from August and down 0.9 percent from September’s $328,000. For October DataQuick showed the first year-over-year price rise in three years. Case-Shiller’s October figures won’t be released until next month.

Nationally, 11 of the 20 metro areas in the Case-Shiller index were up from August to September, with depressed Detroit and relatively healthy Minneapolis up the most, 1.8 percent. On a year-over-year basis, all were down; Denver and Dallas were off the least, down 1.2 percent each.

The national index for the third quarter stood at 137.19, up 3.1 percent from the second quarter but down 8.9 percent from a year earlier.

“We have seen broad improvement in home prices in most of the past six months,” David M. Blitzer, S&P’s index committee chairman, said in a statement.

But S&P Vice President Maureen Maitland told The New York Times yesterday that she worried about a “W”-shaped trend in home prices — they’ve fallen from the peak, risen a bit from the trough and now might fall again before rising once more.

“This may be a bit of a transition period,” Maitland said.

The index improved for the sixth straight month for San Francisco and Washington and for the fifth consecutive month for San Diego, as well as Chicago and Minneapolis. Las Vegas remained the most depressed market, with prices having fallen 37 straight months and seeing a peak-to-trough plunge of 55.4 percent. Detroit prices are improving but are still 73 percent off their 2000 value. Top-ranked Washington is 80 percent higher than at the beginning of the decade.

A separate report released by the National Association of Home Builders indicated declining affordability as prices improve in various markets. For San Diego, 50.2 percent of homes sold in the third quarter were affordable to households earning the median income of $74,900, down from 56 percent in the second quarter and a cyclical high of 58.8 percent in the first quarter. The latest quarterly median home price was $300,000, up $15,000 from the second quarter and $30,000 from the first quarter.

San Diego ranks as the 19th least-affordable market out of 185 areas surveyed. The New York City metro area, with a median of price of $425,000 and household income of $64,800, was the least affordable at 19.2 percent. Las Vegas, with a median of $130,000 and income of $65,400, was the most affordable at 84.7 percent.

Nationally, the affordability rate was 70.1 percent for a median price of $179,000 and median income of $64,000. California’s affordability stood at 59.1 percent, based on a median price of $232,500 and household income of $70,400.

Liz Snow, chief executive of the California Building Industry Association, said in a statement that the latest affordability figures reflect increasing competition among bargain-hunting buyers.

“While we’re not out of the woods yet, this could signal that the bottom of the market is here,” Snow said, “and as the market improves, we could be facing an imbalance in supply and demand.”